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- PDB-3oa3: Crystal structure of a putative deoxyribose-phosphate aldolase fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3oa3 | ||||||
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Title | Crystal structure of a putative deoxyribose-phosphate aldolase from Coccidioides immitis | ||||||
![]() | aldolase![]() | ||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() deoxyribose phosphate catabolic process / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
![]() | ![]() Title: Crystal structure of an unknown aldolase from Coccidioides immitis Authors: Edwards, T.E. / Gardberg, A.S. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 208.8 KB | Display | ![]() |
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PDB format | ![]() | 167.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3ngjS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 31187.299 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: E0CX06*PLUS, ![]() #2: Chemical | ![]() #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.99 % |
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Crystal grow![]() | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 4.93 mg/mL CoimA.00559.a.A1 PS00460 against Hampton Index Screen condition G9, 0.2 M ammonium sulphate, 0.1 M Tris pH 8.5, 25% PEG 3350 enheanced with 20% glycerol as cryo-protectant, ...Details: 4.93 mg/mL CoimA.00559.a.A1 PS00460 against Hampton Index Screen condition G9, 0.2 M ammonium sulphate, 0.1 M Tris pH 8.5, 25% PEG 3350 enheanced with 20% glycerol as cryo-protectant, crystal tracking ID 216774g9, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 31, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→50 Å / Num. all: 69876 / Num. obs: 68464 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 23.315 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 19.41 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing![]() | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 52.64 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3NGJ molecule A Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.1915 / WRfactor Rwork: 0.1621 / Occupancy max: 1 / Occupancy min: 0.19 / FOM work R set: 0.9013 / SU B: 2.844 / SU ML: 0.046 / SU R Cruickshank DPI: 0.0817 / SU Rfree: 0.0831 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 53.66 Å2 / Biso mean: 21.0965 Å2 / Biso min: 9.07 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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